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Bioconductor Changlog.
Tue, 13 Oct 2009
biocViews
final changes to the ontology based on suggestions in the bioc phone conference
adding the sqlLite database to the repository. The updateVocab script will update the db when the package is edited
biocViews
Added vignette R scripts to package home pages.
biocViews
Bumped pkg versions for BioC 2.5 devel line.
Bumped pkg versions for BioC 2.4 release.
biocViews
Added terms to describe custom CDFs and custom schemas
Added another term for another alternate CDF schema as well as a term
to describe custom schemas for annotation packages based on foreign
database schemas. For all standard annotation packages, there is
already a way to determine and inspect that schema inside of
AnnotationDbi, but for foreign schemas there needs to be a term to
indicate that things are based on a different underlying design.
biocViews
Updated biocView data after removal of DNACopyNumber term.
Removed DNACopyNumber from terms. Was a duplication.
biocViews
added a couple of lines to updateVocab.sh to generate SQLite DB of the onthology tree. Also rearanged some of the terms as suggested by Vince and Robert
biocViews
Update biocViews database.
Updated the sqltable.
biocViews
updated biocview names for statistics to statistics/bioinformatics and computational domains to computation/infrastructure, also moved preprocessing adn quality control under statistics /bioinformatics
Updated package details man page.
biocViews
Support multiple repository URLs to search through.
Remove concatenation of dependsOnMe and suggestsMe slots for PackageDetails objects.
Changed name of argument from reposFullRoot to reposFullUrl.
biocViews
updated serialized graph object
biocViews
Add vocabularies -- Colon, Lung, Kidney, E.ColiData and FlowCytData --
onto ExperimentData.
biocViews
Adding Biobase to the Suggests field.
Added Imports Me information to package pages.
Cleaned up the dependency structure of biocViews.
biocViews
Removed usage (or reference) to pstricks tex style in BioC vignettes.
biocViews
Updated biocViews database.
Remove bad format tag.
biocViews
Added a MultiChannel category to Microarray.
biocViews
Added hooks to support usage of the bioconductor changelogs.
Adding more informative label to download history.
Minor change to handling of download history.
Fixing the passing of the HTML link for the download statistics.
FIxed download stats link.
Updating biocViews to include hooks for download statistics.
biocViews
Added a data representation infrastructure subview.
Simplifying the structure.
Update the hierarchy.
biocViews
Adding reference manuals to man pages.
Switched to using vignette index entries in package home pages.
biocViews
bumping version number
added new term sequencing and rearranged some of the existing ones
biocViews
Minor change to extractNAMESPACEFromTarball. Explicitly use the --wildcards flag to tar command call.
biocViews
added package help page
added term FlowCytometrtry, fixed broken links in documentation and added a couple of lines to the vignette how to list available terms using getSubTerms
biocViews
Save data in sqlite2 format.
Added DNACopyNumber to the biocViews ontology.
biocViews
Added within repository package links in Depends, Imports, Suggests, dependsOnMe, and suggestsMe fields on package home pages.
biocViews
fixed examples and Vignette to reflect new onthology
biocViews
Added term for GUI
This term is being added primarily to indicate that a package has
implemented a full blown GUI with menus etc.
biocViews
Cleaned up the dependency structure of biocViews.
biocViews
removed quotes from do.call
biocViews
Make Rnw file extension case insensitive when managing vignettes.
Made the Rd file extension case insensitive in the pdf reference manual construction function.
biocViews
Minor change to extractVignettes. Explicitly use the --wildcards flag to tar command call.
biocViews
Bumping version numbers for BioC 2.4 devel.
Bumping version numbers for BioC 2.3 release.
biocViews
Separated Documentation from Package Download tables from package home pages.
biocViews
Fixed a typo.
Added an infrastructure to control the body background color of the stylesheet.
biocViews
Passing the reposFullRoot argument through writeRepositoryHtml.
Added a new slot to PackageDetail objects to manage links to depends/imports/suggests packages.
Another rev.
Another change to htmlValue.
Fixing a bug in htmlValue.
Fixed a bug in htmlValue.
biocViews
Updating the version number for the trunk post-BioC 2.2 release.
Updating the version number for the BioC 2.2 release.
biocViews
Minor change to extractVignettes. Explicitly use the --wildcards flag to tar command call.
biocViews
Updated data/biocViewsVocab.sqlite and data/biocViewsVocab.rda (by running updateVocab.sh). Bumped version to 1.13.3
Made the following changes to the vocabulary:
- Removed
ExperimentData -> BiologicalDomains;
because we can't have BiologicalDomains under the Software and
ExperimentData top-level views (biocViews currently doesn't allow this).
- Added
SequenceAnnotation -> GenomicSequence;
SequenceAnnotation -> miRNA;
on Marc's request.
- Replaced
ExperimentData -> ChIPchip
by
ExperimentData -> ChIPchipData
because we can't have ChIPchip under the Software and ExperimentData
top-level views (biocViews currently doesn't allow this).
- Replaced
ExperimentData -> HighThroughputSequencing;
by
ExperimentData -> HighThroughputSequencingData;
- Added
AssayTechnologies -> HighThroughputSequencing;
HighThroughputSequencing -> ChIPseq;
HighThroughputSequencing -> RNAseq;
Will be followed by another commit after I find a machine where 'dot2gxl
inst/dot/biocViewsVocab.dot' doesn't segfault (so I can run updateVocab.sh).
biocViews
Adding support for Mac OS X 10.5 Leopard binary packages.